Early-Onset Infection Caused by Escherichia coli Sequence Type 1193 in Late Preterm and Full-Term Neonates

Using whole-genome sequencing, we characterized Escherichia coli strains causing early-onset sepsis (EOS) in 32 neonatal cases from a 2019–2021 prospective multicenter study in France and compared them to E. coli strains collected from vaginal swab specimens from women in third-trimester gestation. We observed no major differences in phylogenetic groups or virulence profiles between the 2 collections. However, sequence type (ST) analysis showed the presence of 6/32 (19%) ST1193 strains causing EOS, the same frequency as in the highly virulent clonal group ST95. Three ST1193 strains caused meningitis, and 3 harbored extended-spectrum β-lactamase. No ST1193 strains were isolated from vaginal swab specimens. Emerging ST1193 appears to be highly prevalent, virulent, and antimicrobial resistant in neonates. However, the physiopathology of EOS caused by ST1193 has not yet been elucidated. Clinicians should be aware of the possible presence of E. coli ST1193 in prenatal and neonatal contexts and provide appropriate monitoring and treatment.


Learning Objectives
Upon completion of this activity, participants will be able to:

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Assess the prevalence and complications of early-onset neonatal sepsis (EOS)

E xtraintestinal pathogenic Escherichia coli and
Streptococcus agalactiae are bacterial pathogens that commonly cause early-onset neonatal sepsis (EOS) in industrialized countries.EOS is confirmed by a blood or cerebrospinal fluid culture positive for the causative pathogen <72 hours after birth.EOS incidence is ≈1/1,000 live births (1,2); 10% of cases are complicated by meningitis, which can lead to neurologic sequelae in up to 50% and death in 10% of cases in industrialized countries (3).
EOS caused by S. agalactiae can be prevented by peripartum antimicrobial prophylaxis but not EOS caused by E. coli.E. coli strains that cause neonatal meningitis have been well characterized, but E. coli strains that cause EOS less so (4,5).Neonatal meningitis E. coli strains belong mainly to phylogenetic group B2/sequence type complex (STc) 95 (6) and are frequently O18:K1, O1:K1, O83:K1, or O45 S88 :K1 serotypes (7,8).Most STc95 strains are distributed worldwide and still largely susceptible to antimicrobials (9).However, other strains that can cause EOS, notably in preterm neonates, might be resistant to probabilistic antimicrobial therapy.In a recent study in Israel (10), maternal carriage rates of extended-spectrum β-lactamase (ESBL)-producing E. coli were 17.5% for mothers and 12.9% for preterm neonates; in China, ESBL accounted for up to 48% of E. coli infections in neonates (11).
Characterizing E. coli strains that cause EOS would constitute a critical first step towards better understanding the pathophysiology of this condition and developing potential preventive strategies.We conducted a prospective study covering a large area in France to estimate annual incidence and pathogen distribution of EOS in neonates born at ≥34 weeks of gestation during 2019-2021 (12).In total, we recorded 107 cases of bacteremia including 35 caused by E. coli, 15 (incidence 0.89/1,000 births) in late-preterm and 20 (0.06/1,000 births) in full-term infants.We prospectively recorded data on maternal and infant demographics, maternal antimicrobial therapy, peripartum antimicrobial prophylaxis, and outcomes (12).We aimed to use whole-genome sequencing (WGS) to characterize E. coli strains that caused EOS in cases from this prospective study and stratify results according to these data.In addition, we determined to compare those strains to E. coli strains obtained from cultures from vaginal swabs collected to screen for S. agalactiae carriage at 34-38 weeks of gestation from woman with newborns who had no history of EOS.The ethics committee institutional review board (Ramsay Santé Recherche & Enseignement, IRB00010835) authorized the study (12).

Bacterial Strains
We recorded 35 cases of EOS caused by E. coli during a prospective study in 81 maternity wards of the Ile de France area during 2019-2021 (12).Thirty-two E. coli isolates were sent to the National Reference Center in Robert-Debré Hospital to be further characterized.For comparison with the isolates from the Using whole-genome sequencing, we characterized Escherichia coli strains causing early-onset sepsis (EOS) in 32 neonatal cases from a 2019-2021 prospective multicenter study in France and compared them to E. coli strains collected from vaginal swab specimens from women in third-trimester gestation.We observed no major differences in phylogenetic groups or virulence profiles between the 2 collections.However, sequence type (ST) analysis showed the presence of 6/32 (19%) ST1193 strains causing EOS, the same frequency as in the highly virulent clonal group ST95.Three ST1193 strains caused meningitis, and 3 harbored extended-spectrum β-lactamase.No ST1193 strains were isolated from vaginal swab specimens.Emerging ST1193 appears to be highly prevalent, virulent, and antimicrobial resistant in neonates.However, the physiopathology of EOS caused by ST1193 has not yet been elucidated.Clinicians should be aware of the possible presence of E. coli ST1193 in prenatal and neonatal contexts and provide appropriate monitoring and treatment.
Ile de France study, we included 50 E. coli isolates obtained from cultures from vaginal swabs collected from 4 maternity wards to screen pregnant woman for S. agalactiae carriage at 34-38 weeks of gestation.We found healthy vaginal carriage (HVC) among all; that is, none of the infants of the pregnant women from the S. agalactiae screening developed EOS caused by E. coli.

Bacterial Collection and Demographic and Clinical Features of Patients
We studied 82 E. coli isolates.Birth locations of the neonates within Ile de France were diverse (30 different locations among 32 EOS case-patients).Babies were delivered at full term (≥37 weeks of gestation) in 59% (19/32) and preterm (<37 weeks of gestation) in 41% (13/32) of cases.In 6 (31%) cases from the full-term group and 7 cases (54%) from the preterm group, mothers received antimicrobial treatment <3 days before labor.We observed 6 cases of meningitis, 3 each from the full-term and preterm neonate groups (Table 1).

Diversity and Phylogenetics of EOS and HVC E. coli Strain Collections
Five of 7 major E. coli phylogroups-A, B1, B2, D, and F, but not C or E-were represented in similar proportions in both the Ile de France study and vaginal swab collections (p>0.05).The exceptions to this trend were phylogroup A being more common in vaginal swab (22%) than EOS (9.4%) isolates and group B2 more common in EOS (65.6%) than vaginal swab (48%) isolates (Figure 1).Among the 3 most frequent ST/STc variants in our study, STc10 (phylogroup A) was present in more HVC strains, whereas ST95 and STc14 (phylogroup B2) were more common in EOS strains.The imbalance was striking for STc14, which was present in 25% of EOS strains but only 4% of HVC strains (p = 0.01) (Figure 2).STc14 isolates included 6 ST1193, 2 ST14, and 2 ST404.Of note, the 6 ST1193 isolates were found exclusively in the EOS collection.

Main Features of EOS Caused by ST1193 E. coli and Characterization of Isolates
All 6 ST1193 EOS strains were isolated from different maternity hospitals.Half (3/6) of neonates with ST1193 EOS were born at full term.Three neonates had meningitis, 2 full-term and 1 preterm.Four (67%) mothers with ST1193 strains received prenatal antimicrobial therapy compared with nine (35%) for the non-ST1193 strains (p>0.05)(Table 1; Figure 6).All strains were resistant to fluoroquinolones, 3 were resistant to azithromycin, and 3 others harbored an ESBL phenotype (Table 2).All strains were lactose nonfermenters (data not shown).

Discussion
In our study, we used WGS to characterize E. coli strains causing EOS from a prospective multicenter study in France ( 12) and compared them to E. coli strains obtained from vaginal samples from pregnant women at 34-38 weeks of gestation.Although we observed no major differences between the EOS study and vaginal sample collections in distribution of phylogroups or virulence factors except the K1 antigen, we identified emerging ST1193 strains as major causes of EOS.Three isolates of the ST1193 clonal group caused meningitis, and half harbored an ESBL.E. coli ST1193 thus appears to be the most virulent and antimicrobial-resistant E. coli group that causes EOS.
Among major phylogroups, B2 and, to a lesser extent, D are associated with extraintestinal infections, whereas A and B1 are most associated with commensal strains or intestinal infections (15).We also observed predominance of B2 strains in our EOS population, regardless of the term of birth of the newborns.Although the proportion of phylogroup A strains was higher in the HVC than the EOS population, B2 strains largely predominated in the HVC collection, as reported in previous studies (16,17).However, sequence typing enabled a finer comparison between the 2 collections.Among the HVC strains, phylogroup A/STc10 (ST10, ST13795, ST6826, and ST13957) was predominant but was rarely observed among the EOS patients, in which ST95 and STc14 (notably ST14 and ST1193) were largely predominant.The high frequency of ST95 was expected because of its virulence in neonates, notably those with neonatal meningitis, which is well known worldwide (6,18).Of note, ST95 was second most common among HVC strains, suggesting its capacity to colonize the vagina, at least temporarily.Five of 6 mothers with EOS caused by ST95 received no prepartum antimicrobials.
In contrast, ST14 and ST1193 strains were frequently associated with women receiving prepartum antimicrobials (5/8), and those strains were not present among HVC patients, suggesting the vaginal environment might inhibit the presence of ST14 and ST1193 strains.Of note, STc14 but not ST95 was more prevalent among preterm neonates with EOS, and 3/6 infections caused by ST1193 strains occurred in preterm newborns.It might be that ST1193 strains are less virulent than ST95 strains commonly found in full-term neonates.However, almost all women with preterm newborns received antimicrobial drugs, which might favor the selection of resistant strains, such as ST1193.
One study observed an increased rate of ST1193 causing bloodstream infections, mostly in elderly patients in Canada during 2016-2018 (22).In an analysis of the population structure of 218 ESBL-producing E. coli in urinary tract infections in febrile children in France during 2014-2017, we noted prevalence of ST1193 rose from 0% to 9% (23).Large epidemiologic studies of ST1193 prevalence in neonatal infection have only recently been conducted.In 2 studies, ST1193 was shown to be a major cause of neonatal sepsis; however, because the definition of EOS in those studies differed from ours, data are difficult to compare (11,24).The finding of a worrying percentage of ST1193 among EOS patients (19%) in our study population indicates that in the future that ST should be closely monitored using microbiologic detection.
One epidemiologic study of intracranial infections in neonates caused by E. coli (25) found ST1193 to be the most prevalent ST (28%).All 8 ST1193 isolates caused late-onset infections, although none caused EOS.Only 1 recent case of early-onset meningitis caused by E. coli ST1193 has been reported, but cases of meningitis caused by ST1193 occurring >72 hours after birth were described in another study (24,26).The recent case occurred in a late-preterm neonate with a history of prolonged rupture of the membrane with prepartum and peripartum antimicrobial drugs administered, as in most of our cases.
Given that 3/6 ST1193 strains caused neonatal meningitis, such strains were shown to have high invasive disease potential in newborns.Several virulence factors and genetic determinants have been shown to be involved in the pathophysiology of neonatal meningitis, such as capsule K1, siderophore salmochelin, plasmid pS88, and invasin IbeA (27).Of note, among these determinants, only the K1 capsule was present in the ST1193 strains.Several virulence factors (Iha, Imm, plasmid-encoded enterotoxin SenB, Sat) were present in all ST1193 strains, with a significant p value (p<0.05)compared with non-ST1193 (Appendix Table 2) strains, and were present in >85% of ST1193 strains in the large collection of 1 study (28).Therefore, without in vivo study, it is difficult to determine the specific roles of these key factors in the invasiveness of ST1193 in cerebrospinal fluid.Except for consistency of fluoroquinolone resistance and carrying the fimH64 allele, which characterized all ST1193 E. coli strains described in previous studies, multiple plasmid-borne resistance genes have been reported but are inconsistently associated with ST1193 (19,28,29).No isolates harbored the same phenotypic antimicrobial resistance pattern, highlighting their diversity.The co-occurrence of bla CTX-M-15 /bla OXA-1 / aac(6′)-Ib-cr, which we observed in 3/6 of EOS strains, has been frequently described, initially in ST131 but also more recently in emerging lineages of ST1193 (30).Half of our strains, similar to findings from other studies (28), carried the mphA resistance gene and had a high azithromycin MIC (>32 mg/L) (data not shown), which might have contributed to the emergence of ST1193 given that azithromycin is among the most-prescribed antimicrobial drugs worldwide among adult outpatients (31).
As of May 2023, sequences of 2,031 E. coli ST1193 strains from all over the world are available in Enterobase (13).Of those, 80% belong to HC20 571, as did our strains, and most (82%) harbor rMLST 1674, whereas rMLST 33503 is found in only 8%.Hierarchical clustering analysis did not suggest the presence of a particular clone in our collection.Distribution of rMLSTs was notably different: half of our ST1193 strains belonged to rMLST 33503.Whether this subgroup is emerging or has specific invasive disease potential in neonates has yet to be determined.
Among its strengths, our prospective epidemiologic study, conducted in a large area of France, estimated annual incidence and pathogen distribution in EOS patients (12) and documented the unique molecular and phenotypic characteristics of the strains in our study.We were limited by the small number of patients; results, especially implication of ST1193 in infections in very preterm neonates, need to be confirmed in larger study populations.
In conclusion, our findings suggest that ST1193 is emerging as a major E. coli pathogen that can cause EOS and early-onset neonatal meningitis in full-term and late-preterm newborns and might surpass ST95 in incidence and causing illness because of its potential virulence combined with its resistance to multiple antimicrobials.Pediatricians and microbiologists should be aware of the public health threat from E. coli ST1193 and the benefits of prepartum/peripartum EOS treatment with effective antimicrobials.Isolating ST1193 E. coli strains in the neonatal context (from mother, newborn, or both) will require careful, sustained clinical monitoring of newborns.It might also require implementing measures to limit spread, especially in neonatal wards.On the basis of microbiologic evidence, ST1193 should be suspected when 3 properties are all present: high resistance to ciprofloxacin, K1 capsule, and non-lactosefermenting colonies, each of which can easily be tested for in a microbiology laboratory.Further studies should help to define the genetic determinants of ST1193 virulence in neonates and confirm and subsequently explain its inability or weak ability to colonize the vagina.Clinicians need to be aware of the possible presence of E. coli ST1193 in prenatal and neonatal contexts and provide appropriate monitoring and treatment.

*
ESBL, extended spectrum -lactamase; FimH, type 1 fimbriae D-mannose specific adhesin; ID, identification; Ku, unknown serogroup capsular; +, positive for condition; -, negative for condition.†ForParis birthplaces, name of hospital where born is indicated in parentheses.‡Amoxicillin was the only antimicrobial prescribed within 3 days before labor.§Early onset neonatal meningitis.¶O antigen predicted with SerotypeFinder 2.0 and serogroup capsular predicted by the Center for Genomic Epidemiology (https://genomicepidemiology.org).#Sequence type complex (STc) indicated in parentheses if different from ST number.

Figure 1 .
Figure 1.Phylogroup distribution among 32 EOS Escherichia coli strains from neonates and 50 HVC strains, France.No significant difference was observed in each group.EOS, early-onset neonatal sepsis; HVC, healthy vaginal carriage.

Figure 5 .
Figure 5. ST distributions according to birth term among 32 neonates with early-onset neonatal sepsis.ST, sequence type.

Figure 6 .
Figure 6.Distribution of maternal antimicrobial therapy within 3 days before delivery according to Escherichia coli ST among 32 neonates with earlyonset neonatal sepsis, France.ST, sequence type.

Table 1 .
Characteristics of mothers and their newborns with early-onset sepsis caused by Escherichia coli strains, France*

Table 2 .
Characteristics of newborns with early onset sepsis caused by ST1193 Escherichia coli and genetic and phenotypic features of the isolates* †Term of pregnancy at birth in weeks.‡Antimicrobialtreatmentwithin 3 days before labor began.§Searchfor antimicrobial resistance genes and replicon/plasmid sequence types run using Center for Genomic Epidemiology website (https://genomicepidemiology.org) and local BLAST.¶Hierarchicalclustering of distances between genomes calculated using 10 (HC10) or 20 (HC20) shared core genome MLST alleles and genomes linked on a single-linkage clustering criteria.#Approach that indexes variation of the 53 genes encoding the bacterial ribosome protein subunits.